I'm resurrecting this thread because I've since done some more touring and the scuffing/abrasion problem to the inner chain stays has not reoccurred. The initial tour was in Spring of 2012, and there was some mud at that time. I suspect it was the mud that caused the abrasion. This didn't occur to me initially because I was thinking that the rim brakes would have wiped all the mud off. But the rim brakes only touch the rim (duh..) and not the tires. So the mud (and grit inside the mud) that collected on the outsides of the tires would have been carried around and wiped against the chainstays and that is what caused the abrasion.
My subsequent tours were in dry weather. There was plenty of dust, but no mud. Upon inspecting the inner chainstays today, I noticed the touch-up paint I applied to those abraded areas after that initial tour is still mostly intact, though there are some scratch marks, perhaps from pebbles carried in the knobs on the sides of the tire.
Anyway, this clears up the mystery. I don't think this sort of abrasion can be avoided. My general feeling at this point, after 5000 miles and several months of touring on rugged dirt roads, is I don't really care if the frame or rear racks and other supposedly unlimited-lifetime components wear out eventually. Just buy replacements. Bicycles are cheap in the grand scheme of things, even expensive bikes like Thorn and expensive components like Rohloff. Certainly far cheaper than motor vehicles, houses, medical insurance and other big ticket items that some people buy but I am able to avoid buying.